All Tutorials

  • Tue Mar 11, 1:30 pm - 3:00 pm
    575
    Walter Library

    The Crystallographic Object-Oriented Toolkit (Coot) is a free academic software package mainly used by crystallographers to build, manipulate, and validate protein structures. Coot is similar to programs like O and Insight II in functionality, with the advantage of having many of the building and validation features automated. Coot also has the added benefit of being able to read the main binary files of CCP4 (.mtz files) directly to allow for easy map creation and refinement of the structure.


    This hands-on tutorial will bring the user up to speed using the Coot software for model building, manipulation, and validation.


  • Tue Mar 4, 1:00 pm - 3:00 pm
    575
    Walter Library

    This is a hands-on workshop introducing relational databases and structural query language (SQL). Attendees will practice creating and querying databases in an Oracle environment. Topics include a brief overview of relational database design concepts and principals, and conceptual data models and constraints.


  • Thu Feb 28, 1:00 pm - 3:00 pm
    138
    Cargill Building

    With the development of genomics and proteomics, many biologists now need to handle large amounts of data for their research. Bioinformatics programming, especially Perl programming, is well-suited for biological data manipulation and analysis.


    This tutorial will introduce the fundamental concepts and mechanisms of computer programs, using Perl language as an example. We will use practical program examples such as transcription, translation, sequence retrieval, promoter sequence extraction from genomic DNA, motif scanning, parse BLAST results, etc., to demonstrate how bioinformatics programming can make your work easier and more efficient.


  • Tue Feb 26, 1:00 pm - 3:00 pm
    402
    Walter Library

    GAMESS is a program that can be used to calculate a variety of chemical properties. GAMESS is primarily used for carrying out electronic structure calculations. This tutorial includes an overview of the program's capabilities, a detailed description of how to run the program at MSI, and tips on how to run jobs efficiently.


  • Thu Feb 21, 1:00 pm - 3:00 pm
    575
    Walter Library

    GeneSpring is one of the most widely used microarray software package for both one-channel and two-channel microarray data analysis. Besides the basic statistical methods, it shows strength in various normalizations, gene annotation and gene ontology analysis, and user-friendly visualizations.


    This tutorial will demonstrate various capabilities of GeneSpring including genome installation, data loading, experiment creation, normalization, filtering, clustering, group comparisons, gene list Venn diagrams, and gene ontology, class prediction tool, gene ontology, pathway, Scripts, etc.


  • Tue Feb 19, 1:00 pm - 3:00 pm
    402
    Walter Library

    Microarray is a powerful technology for biological exploration which enables researchers to simultaneously measure the level of activity of thousands of genes. It is becoming a routine experimental technique for life science research.


    This tutorial will present an overview of this technology including different microarray platforms, array design, data acquisition, data normalization, data analysis, and gene list interpretation. We will also introduce and compare several microarray software tools that MSI hosts.


  • Thu Feb 14, 1:00 pm - 3:00 pm
    575
    Walter Library

    Amira is a powerful visualization software package that enables data manipulation, geometry creation, and viewing in a meaningful format. This tutorial will describe the modular approach in Amira to build a visualization framework for different scientific data types. We will introduce concepts in computational geometry, modeling, and surfaces and volume rendering in Amira. This tutorial serves varying interest groups including medicine, biology, chemistry, physics, material sciences, geophysics, astronomy, and engineering.


  • Tue Feb 12, 1:00 pm - 3:00 pm
    402
    Walter Library

    In recent years, mass spectrometry has been recognized as one of the most successful techniques in proteomics research, playing a fundamental and indispensable role in current proteomic laboratories. This tutorial will review current computational tools in mass spectrometry data analysis and show a detailed MS data analysis workflow, including spectrum reconstruction, peptide and protein identification, protein function annotation, function prediction for hypothetical proteins, data mining of quantitation MS data, and downstream bioinformatics analysis. All the corresponding computation tools will be discussed.


  • Thu Feb 7, 1:00 pm - 3:00 pm
    575
    Walter Library

    Trying to discover patterns in data? Looking for techniques for classification and prediction? In this hands-on tutorial, we will show you how to accomplish these data-mining tasks using Weka. Weka is a freely available software package for knowledge analysis and pattern discovery that contains tools for data preprocessing, classification, regression, clustering, association rules, and visualization.


    In this tutorial, we go through the basic steps involved in loading data into Weka, exploring and filtering data, and applying Weka data-mining tools. The main focus is on techniques for classification, such as decision trees or neural nets, but we will also explore the other capabilities of Weka (clustering, association analysis, etc.) as time allows.


  • Tue Feb 5, 1:00 pm - 3:00 pm
    575
    Walter Library

    Perl is a scripting language that can make writing and maintaining scripts for various UNIX tasks considerably easier than using one of the many shell languages. For example, Perl is very useful for retrieving output from files of completed jobs for use in reports, input to subsequent jobs, and so forth. Perl scripts are often very portable, since Perl is supported on virtually all computer platforms. Perl scripts can be extremely simple or complicated and powerful.


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